The atlas names the Louvre as the custodian of objects and not as a religious body, and the word custodian is doing careful work. How several of the objects reached Paris is part of the record, and it is not agreed.
The routes are various. Some arrived through the seizures of the revolutionary and Napoleonic campaigns, a large part of which were returned after 1815 while some were not. Some arrived through nineteenth century excavation conducted under permits issued by the Ottoman Empire or by Egypt, in a legal framework that allowed the excavator to keep a share and that no source country would agree to today. The Dendera zodiac was cut out of the temple ceiling in the early 1820s by a private expedition and sold on, and Egypt has publicly asked for it back. Others were bought on the market, given, or came through French archaeological missions abroad.
The museum, the source countries and the scholarship do not agree about what should follow from any of that, and the disagreement covers law, ethics and practical custody in different proportions for different objects. There is also a separate and continuing programme of research into works that changed hands under the Nazi occupation, some of which the museum holds pending identification of their owners.
The atlas does not resolve any of this. It records that the objects are here, and that where they should be is contested.